Type traits and mammary health are important traits for dairy ruminant breeding. They govern animal health, milking ability and longevity as well as the economic sustainability of farms. However, little is known about the genomic regions controlling these traits in goat. We report here a genome-wide association study in dairy goats for eleven type traits, and SCC, as a proxy for mastitis resistance. The analysis was implemented using a daughter design composed of 1941 Alpine and Saanen goats sired by 20 AI bucks and genotyped with the goatSNP50 chip. Both linkage analyses (LA) and linkage disequilibrium (LD) using interval mapping were performed and the two breeds were analysed together and separately. A large number of QTL regions was highlighted, suggesting that the genomic control of type and SCC traits is highly polygenic in goats. Moreover, the regions found were different between Alpine and Saanen, revealing a breed-specific control. The Capra hircus autosome (CHI) 19 appeared to be especially enriched in SNPs associated with type and SCC, with two highly significant regions in the Saanen breed. The first region is located between 33 and 42 Mb on CHI 19 and was significantly associated with SCC. This interval contains or is in close proximity to candidate genes that could be involved in response to intra-mammary infections (RARA, STAT3, STAT5a and STAT5b). The second region, located between 24.5 and 27 Mb on CHI 19 was associated with udder type traits (udder floor position and rear udder attachment) in the same interval that had been associated previously with milk production traits. This region and its potential pleotropic effects is currently under investigation. Altogether, these results will be helpful for goat selection in the future. It indicates that a within-breed genomic selection should be favoured for those traits in French goat and open the way to the identification of causal mutations.