In this cross-sectional study, prevalence of clinical mastitis (PCM) and farm-specific risk factors were determined on 531 doe rabbit farms in Spain and Portugal, from January 2001 through March 2017. The information was obtained by carrying out 2367 visits and doing physical examinations of 144,455 lactating does, sorted in 2635 cohorts. Overall mean PCM was 4.05% (CI95% [3.87–4.22]), (minimum to maximum: 0–36.00% PCM). This study suggests that PCM was influenced by the variable number of batches (a batch was a group of does served the same day), per maternity barn (p < 0.0001). The duo system (does being moved to clean disinfected barns for parturition), was also an enabling risk factor for CM. The day of service or lactation stage also affected PCM. Lastly, there was an effect of the breeds or lines (p < 0.0001); mean PCM ranged between 1.29% and 7.09%. A subset of data obtained from 200 farms visited during January 2012–March 2017, was recorded to describe the use of antimicrobials against mastitis. Changes in host, husbandry, environment, and biosecurity practices, are highlighted to provide health and welfare benefits for breeding rabbits.