Using whole genome sequencing, we could not identify variants in protein function affecting regions of the candidate genes CPAMD8 and NID1 which gave evidence for strong association of homozygous mutant genotypes with congenital cataracts in Holsteins from farm C. We did also not find private homozygous intronic variants in the regions of bovine candidate genes CPAMD8 and NID1 for these congenital cataract cases. Here, NID1 is linked to early-onset non-syndromic cataract.