The compression you select absolutely makes a difference in the quality of the rendered footage. But that doesn't mean that the problem is automatically related to that. "Video" is not a high quality codec though, and you might Try Uncompressed or the Quicktime Animation codec to see if those give you better results. Files will be bigger though, just so you are aware.
The amount of filters you have applied to the footage or any resizing, as Darth Stazz mentioned, could also factor into this.
Sometimes people with similar questions are also just seeing Interlacing lines,
which aren't a problem but are part of how video works. They are, however, difficult to fully understand sometimes.