Systematic whole genome sequencing provides a rapid and powerful method to identify recent novel mutations on a cattle population scale. It helps farmers to detect early carriers of new genetic anomalies and more generally to boost genomic selection. Regarding genetic defects, the aim is to identify new candidate mutations that may have deleterious potential before they are widely spread in the population to inform the breeders. A major drawback is the high rate of false positives, ie of variants with a strong annotation but without any effect. Therefore the annotation is the most critical step. We focussed only on still unknown variants (ie de novo or likely very recent mutations) in highly conserved sequences in other species and/or with effects predicted to be similar to those described in OMIM or MGI databases. We applied this strategy on whole genome sequences on 571 artificial insemination bulls from to 14 dairy and beef breeds. In large breeds, recently marketed bulls were selected. In smaller breeds, influential ancestors not yet sequenced were chosen. In total, we identified 1548 novel genomic variants with a potential link to certain quantitative traits of interest or possible genetic abnormalities. These variants were investigated by searching for carrier or homozygous descendants, and by adding these variants on the custom part of the EuroGenomics SNP chip for an easy screening of the population. This information is also returned back to bull’s owners, with a specific alert only for the few most critical variants. Although the annotation still lacks accuracy, we believe that whole genome sequencing of all artificial insemination bulls is an early, rapid and always cheaper method for identifying genetic defects before they disseminate in the population. The SeqOccIn project was funded by the Occitanie region, FEDER, and Apis-Gene.