diff --git a/src/gl/stereo3d/gl_interleaved3d.cpp b/src/gl/stereo3d/gl_interleaved3d.cpp
index fd7a6c4c6..225f52819 100644
--- a/src/gl/stereo3d/gl_interleaved3d.cpp
+++ b/src/gl/stereo3d/gl_interleaved3d.cpp
@@ -99,7 +99,10 @@ void RowInterleaved3D::Present() const
 		GLRenderer->mScreenViewport.width / (float)GLRenderer->mBuffers->GetWidth(),
 		GLRenderer->mScreenViewport.height / (float)GLRenderer->mBuffers->GetHeight());
 
-	GLRenderer->mPresent3dRowShader->VerticalPixelOffset.Set(0); // fixme: vary with window location
+	GLRenderer->mPresent3dRowShader->VerticalPixelOffset.Set(
+		0 // fixme: vary with window location
+		+ box.height % 2 // because we want the top pixel offset, but gl_FragCoord.y is the bottom pixel offset
+	);
 
 	GLRenderer->RenderScreenQuad();
 }
diff --git a/wadsrc/static/shaders/glsl/present_row3d.fp b/wadsrc/static/shaders/glsl/present_row3d.fp
index 73a01539b..8ae72d1e0 100644
--- a/wadsrc/static/shaders/glsl/present_row3d.fp
+++ b/wadsrc/static/shaders/glsl/present_row3d.fp
@@ -7,7 +7,6 @@ uniform sampler2D RightEyeTexture;
 uniform float InvGamma;
 uniform float Contrast;
 uniform float Brightness;
-uniform int WindowHeight;
 uniform int VerticalPixelOffset; // top-of-window might not be top-of-screen
 
 vec4 ApplyGamma(vec4 c)
@@ -20,8 +19,10 @@ vec4 ApplyGamma(vec4 c)
 
 void main()
 {
-	int thisVerticalPixel = int(gl_FragCoord.y);
-	bool isLeftEye = (thisVerticalPixel + VerticalPixelOffset) % 2 == 0;
+	int thisVerticalPixel = int(gl_FragCoord.y + 1.0); // Bottom row is typically the right eye, when WindowHeight is even
+	bool isLeftEye = (thisVerticalPixel // because we want to alternate eye view on each row
+		 + VerticalPixelOffset // because the window might not be aligned to the screen
+		) % 2 == 0;
 	vec4 inputColor;
 	if (isLeftEye) {
 		inputColor = texture(LeftEyeTexture, TexCoord);