diff --git a/src/TypeScriptProgram.ts b/src/TypeScriptProgram.ts
index abdeb5d..6d6bb00 100644
--- a/src/TypeScriptProgram.ts
+++ b/src/TypeScriptProgram.ts
@@ -1,5 +1,6 @@
 import * as path from 'path';
 import * as ts from 'typescript';
+import NormalizedPath from './types/NormalizedPath';
 
 // Helper class for interacting with TypeScript
 export default class TypeScriptProgram {
@@ -7,9 +8,9 @@ export default class TypeScriptProgram {
     private compilerHost: ts.CompilerHost;
     private program: ts.Program;
 
-    constructor(configFile: string) {
+    constructor(configFile: NormalizedPath) {
         // Parse the config file
-        const projectPath = path.dirname(path.resolve(configFile));
+        const projectPath = path.dirname(configFile);
         const config = readConfigFile(configFile);
         const parsedConfig = ts.parseJsonConfigFileContent(config, ts.sys, projectPath);
         this.compilerOptions = parsedConfig.options;
@@ -32,16 +33,16 @@ export default class TypeScriptProgram {
     }
 
     // Get all imports from a given file
-    getImportsForFile(fileName: string) {
+    getImportsForFile(fileName: NormalizedPath) {
         let fileInfo = ts.preProcessFile(ts.sys.readFile(fileName), true, true);
         return fileInfo.importedFiles;
     }
 
     // Resolve an imported module
-    resolveImportFromFile(moduleName: string, containingFile: string) {
+    resolveImportFromFile(moduleName: string, containingFile: NormalizedPath) {
         const resolvedFile = ts.resolveModuleName(
             moduleName,
-            containingFile,
+            containingFile.replace(/\\/g, '/'), // TypeScript doesn't like backslashes here
             this.compilerOptions,
             this.compilerHost,
             null // TODO: provide a module resolution cache
@@ -51,7 +52,7 @@ export default class TypeScriptProgram {
     }
 }
 
-function readConfigFile(configFile: string) {
+function readConfigFile(configFile: NormalizedPath) {
     const { config, error } = ts.readConfigFile(configFile, ts.sys.readFile);
 
     if (error) {
diff --git a/src/fileMatchesConfigGlob.ts b/src/fileMatchesConfigGlob.ts
index 8e5482f..1def1d7 100644
--- a/src/fileMatchesConfigGlob.ts
+++ b/src/fileMatchesConfigGlob.ts
@@ -1,13 +1,22 @@
 import * as path from 'path';
+import NormalizedPath from './types/NormalizedPath';
+import normalizePath from './normalizePath';
 const minimatch = require('minimatch');
 
-export default function fileMatchesConfigGlob(importFile: string, configPath: string, key: string) {
+export default function fileMatchesConfigGlob(
+    importFile: NormalizedPath,
+    configPath: NormalizedPath,
+    key: string
+) {
     // '*' matches all files under the config
     if (key == '*') {
         return true;
     }
 
     // Remove the file extension before matching
-    importFile = importFile.substr(0, importFile.length - path.extname(importFile).length);
-    return minimatch(importFile, path.resolve(configPath, key));
+    importFile = <NormalizedPath>importFile.substr(
+        0,
+        importFile.length - path.extname(importFile).length
+    );
+    return minimatch(importFile, normalizePath(configPath, key));
 }
diff --git a/src/fileMatchesTag.ts b/src/fileMatchesTag.ts
index b603b0e..5c343ea 100644
--- a/src/fileMatchesTag.ts
+++ b/src/fileMatchesTag.ts
@@ -1,7 +1,8 @@
+import NormalizedPath from './types/NormalizedPath';
 import getTagsForFile from './getTagsForFile';
 
 // Returns true if the given file matches any of the given tags
-export default function fileMatchesTag(filePath: string, tags: string | string[]) {
+export default function fileMatchesTag(filePath: NormalizedPath, tags: string | string[]) {
     // '*' matches all files
     if (tags == '*') {
         return true;
diff --git a/src/getAllConfigs.ts b/src/getAllConfigs.ts
index 708a4d3..5a9bb71 100644
--- a/src/getAllConfigs.ts
+++ b/src/getAllConfigs.ts
@@ -2,6 +2,7 @@ import * as fs from 'fs';
 import * as glob from 'glob';
 import * as path from 'path';
 import ConfigSet from './types/ConfigSet';
+import normalizePath from './normalizePath';
 import getOptions from './getOptions';
 
 let configSet: ConfigSet = null;
@@ -11,11 +12,11 @@ export default function getAllConfigs(): ConfigSet {
         configSet = {};
 
         // Glob for configs under the project root directory
-        let files = glob.sync(path.resolve(getOptions().rootDir, '**/fence.json'));
+        let files = glob.sync(normalizePath(getOptions().rootDir, '**/fence.json'));
         files.forEach(file => {
-            let absolutePath = path.resolve(path.dirname(file));
-            configSet[absolutePath] = JSON.parse(fs.readFileSync(file).toString());
-            configSet[absolutePath].path = absolutePath;
+            let configPath = normalizePath(path.dirname(file));
+            configSet[configPath] = JSON.parse(fs.readFileSync(file).toString());
+            configSet[configPath].path = configPath;
         });
     }
 
diff --git a/src/getConfigsForFile.ts b/src/getConfigsForFile.ts
index 71595f0..389e5ea 100644
--- a/src/getConfigsForFile.ts
+++ b/src/getConfigsForFile.ts
@@ -1,13 +1,15 @@
 import * as path from 'path';
 import Config from './types/Config';
+import NormalizedPath from './types/NormalizedPath';
+import normalizePath from './normalizePath';
 import getAllConfigs from './getAllConfigs';
 
 // Returns an array of all the configs that apply to a given file
-export default function getConfigsForFile(filePath: string): Config[] {
+export default function getConfigsForFile(filePath: NormalizedPath): Config[] {
     let allConfigs = getAllConfigs();
     let configsForFile: Config[] = [];
 
-    let pathSegments = path.resolve(path.dirname(filePath)).split(path.sep);
+    let pathSegments = normalizePath(path.dirname(filePath)).split(path.sep);
     while (pathSegments.length) {
         let dirPath = pathSegments.join(path.sep);
         if (allConfigs[dirPath]) {
diff --git a/src/getOptions.ts b/src/getOptions.ts
index 5e7c36f..f63fb44 100644
--- a/src/getOptions.ts
+++ b/src/getOptions.ts
@@ -1,5 +1,5 @@
-import * as path from 'path';
 import Options from './types/Options';
+import normalizePath from './normalizePath';
 
 let options: Options;
 
@@ -11,8 +11,8 @@ export function setOptions(providedOptions: Options) {
     options = providedOptions;
 
     // Normalize and apply defaults
-    options.rootDir = options.rootDir ? path.resolve(options.rootDir) : path.resolve();
+    options.rootDir = normalizePath(options.rootDir || process.cwd());
     options.project = options.project
-        ? path.resolve(options.project)
-        : path.resolve(options.rootDir, 'tsconfig.json');
+        ? normalizePath(options.project)
+        : normalizePath(options.rootDir, 'tsconfig.json');
 }
diff --git a/src/getTagsForFile.ts b/src/getTagsForFile.ts
index f1cd669..fdd977f 100644
--- a/src/getTagsForFile.ts
+++ b/src/getTagsForFile.ts
@@ -1,6 +1,7 @@
+import NormalizedPath from './types/NormalizedPath';
 import getConfigsForFile from './getConfigsForFile';
 
-export default function getTagsForFile(filePath: string): string[] {
+export default function getTagsForFile(filePath: NormalizedPath): string[] {
     let configs = getConfigsForFile(filePath);
     let tags: { [tag: string]: boolean } = {};
 
diff --git a/src/normalizePath.ts b/src/normalizePath.ts
new file mode 100644
index 0000000..3b0ed4b
--- /dev/null
+++ b/src/normalizePath.ts
@@ -0,0 +1,14 @@
+import * as path from 'path';
+import NormalizedPath from './types/NormalizedPath';
+
+export default function normalizePath(...pathSegments: string[]) {
+    // Resolve the raw path to an absolute path
+    let normalizedPath = path.resolve.apply(null, pathSegments);
+
+    // Normalize drive letters to upper case
+    if (normalizedPath.match(/^[a-z]:/)) {
+        normalizedPath = normalizedPath.substr(0, 1).toUpperCase() + normalizedPath.substr(1);
+    }
+
+    return <NormalizedPath>normalizedPath;
+}
diff --git a/src/runner.ts b/src/runner.ts
index ebd8e61..4b3a047 100644
--- a/src/runner.ts
+++ b/src/runner.ts
@@ -2,6 +2,7 @@ import Options from './types/Options';
 import getOptions, { setOptions } from './getOptions';
 import validateFile from './validateFile';
 import TypeScriptProgram from './TypeScriptProgram';
+import normalizePath from './normalizePath';
 
 export function run(options: Options) {
     // Store options so they can be globally available
@@ -11,6 +12,6 @@ export function run(options: Options) {
     let tsProgram = new TypeScriptProgram(getOptions().project);
     let files = tsProgram.getSourceFiles();
     files.forEach(file => {
-        validateFile(file, tsProgram);
+        validateFile(normalizePath(file), tsProgram);
     });
 }
diff --git a/src/types/Config.ts b/src/types/Config.ts
index 05bcc1c..40d4fb1 100644
--- a/src/types/Config.ts
+++ b/src/types/Config.ts
@@ -1,5 +1,7 @@
+import NormalizedPath from './NormalizedPath';
+
 export default interface Config {
-    path: string;
+    path: NormalizedPath;
     tags?: string[];
     exports?: { [files: string]: string | string[] };
 };
diff --git a/src/types/NormalizedPath.ts b/src/types/NormalizedPath.ts
new file mode 100644
index 0000000..4034d03
--- /dev/null
+++ b/src/types/NormalizedPath.ts
@@ -0,0 +1,8 @@
+// Simulate nominal typing
+// https://github.com/Microsoft/TypeScript/issues/202#issuecomment-302402671
+export declare class Nominal<T extends string> {
+    private nominalType: T;
+}
+
+type NormalizedPath = string & Nominal<'Path'>;
+export default NormalizedPath;
diff --git a/src/types/Options.ts b/src/types/Options.ts
index 7788d3a..a48cfc1 100644
--- a/src/types/Options.ts
+++ b/src/types/Options.ts
@@ -1,5 +1,7 @@
+import NormalizedPath from './NormalizedPath';
+
 export default interface Options {
-    project?: string;
-    rootDir?: string;
+    project?: NormalizedPath;
+    rootDir?: NormalizedPath;
     onError?: (message: string) => void;
 };
diff --git a/src/validateFile.ts b/src/validateFile.ts
index 454a6dc..bc030ba 100644
--- a/src/validateFile.ts
+++ b/src/validateFile.ts
@@ -1,12 +1,14 @@
+import NormalizedPath from './types/NormalizedPath';
+import normalizePath from './normalizePath';
 import TypeScriptProgram from './TypeScriptProgram';
 import validateImportIsAccessible from './validateImportIsAccessible';
 
-export default function validateFile(filePath: string, tsProgram: TypeScriptProgram) {
+export default function validateFile(filePath: NormalizedPath, tsProgram: TypeScriptProgram) {
     const importedFiles = tsProgram.getImportsForFile(filePath);
     importedFiles.forEach(importInfo => {
         const resolvedFileName = tsProgram.resolveImportFromFile(importInfo.fileName, filePath);
         if (resolvedFileName) {
-            validateImportIsAccessible(filePath, resolvedFileName);
+            validateImportIsAccessible(filePath, normalizePath(resolvedFileName));
         }
     });
 }
diff --git a/src/validateImportIsAccessible.ts b/src/validateImportIsAccessible.ts
index b92eef0..9ef7f41 100644
--- a/src/validateImportIsAccessible.ts
+++ b/src/validateImportIsAccessible.ts
@@ -1,21 +1,21 @@
 import * as path from 'path';
 import Config from './types/Config';
+import NormalizedPath from './types/NormalizedPath';
 import getConfigsForFile from './getConfigsForFile';
 import fileMatchesConfigGlob from './fileMatchesConfigGlob';
 import fileMatchesTag from './fileMatchesTag';
 import reportError from './reportError';
 
-export default function validateImportIsAccessible(sourceFile: string, importFile: string) {
-    // Make sure we're using absolute paths
-    sourceFile = path.resolve(sourceFile);
-    importFile = path.resolve(importFile);
-
+export default function validateImportIsAccessible(
+    sourceFile: NormalizedPath,
+    importFile: NormalizedPath
+) {
     // Validate against each config that applies to the imported file
     let configsForImport = getConfigsForFile(importFile);
     configsForImport.forEach(config => validateConfig(config, sourceFile, importFile));
 }
 
-function validateConfig(config: Config, sourceFile: string, importFile: string) {
+function validateConfig(config: Config, sourceFile: NormalizedPath, importFile: NormalizedPath) {
     // If the source file is under the config (i.e. the source and import files share the
     // config) then we don't apply the export rules
     if (!path.relative(config.path, sourceFile).startsWith('..')) {
@@ -36,7 +36,7 @@ function validateConfig(config: Config, sourceFile: string, importFile: string)
     reportError(`${sourceFile} is importing inaccessible module ${importFile}`);
 }
 
-function hasMatchingExport(config: Config, sourceFile: string, importFile: string) {
+function hasMatchingExport(config: Config, sourceFile: NormalizedPath, importFile: NormalizedPath) {
     let isExported = false;
     Object.keys(config.exports).forEach(key => {
         let tags = config.exports[key];
diff --git a/test/fileMatchesConfigGlobTests.ts b/test/fileMatchesConfigGlobTests.ts
index be2f1ad..fb1763e 100644
--- a/test/fileMatchesConfigGlobTests.ts
+++ b/test/fileMatchesConfigGlobTests.ts
@@ -1,8 +1,9 @@
 import * as path from 'path';
+import normalizePath from '../src/normalizePath';
 import fileMatchesConfigGlob from '../src/fileMatchesConfigGlob';
 
-const importFilePath = path.resolve(normalize('a\\b\\c\\d\\e\\file.ts'));
-const configPath = path.resolve(normalize('a\\b'));
+const importFilePath = normalizePath(normalize('a\\b\\c\\d\\e\\file.ts'));
+const configPath = normalizePath(normalize('a\\b'));
 
 describe('fileMatchesConfigGlob', () => {
     it('returns false if not a match', () => {