The aim was to study relationships between morbidity, defined through prevalence of diseases of rabbit females, and BCS, and to assess the effect of several risk factors on both morbidity and BCS. Our study was based on individual examinations of 18,510 does in lactation on 103 farms. We evaluated BCS on a linear scale from 1 to 9, with 5 being the optimum. Prevalence of major diseases were 22.7%, 4.0%, and 6.4% for coryza, mastitis, and ulcerative pododermatitis, respectively. In addition, prevalence was 3.0% for diseases of minor presentation, including mange, which had a prevalence of 1.9%. The BCS of the R line (selected for growth) was 5.55 ± 0.14, whereas for the A line (selected for litter size) it was 4.40 ± 0.11. Females with more than 20 kindlings had on average a BCS 0.25 ± 0.07 units less than those in the 12th lactation (P = 0.0002). Optimal BCS 4.60 ± 0.11 was reached during the third lactation week. Sick females had a BCS of 0.6 ± 0.01 units less than healthy females. Females with a footrest had on average a BCS 0.19 ± 0.05 units greater than those without. The absence of footrests was an enabling risk factor for ulcerative pododermatitis, the prevalence of which increased by 53%. Ulcerative pododermatitis was associated (P = 0.045) with diet; females consuming a rich energy diet were prone to having this disorder; 1 SD increase in DE (0.32 MJ) determined an increase in ulcerative pododermatitis prevalence of 0.8 percentage points. Diet was not an enabling risk factor for the other diseases. The genetic type to which a female belongs is a predisposing risk factor of disease; P, V and H were also maternal lines, while S group was exclusively formed by maternal lines. With regard to coryza, the S group had the greatest prevalence (44.0%), followed by A, P, R (19.0 to 21.0%); the V line, selected for prolificacy, showed the least prevalence (12.0%). For the case of mastitis although significant (P < 0.05), the magnitude of the differences between disease prevalence was less; R line had a mastitis prevalence of 11.0% while the least prevalence was observed for V does (4.0%). Simultaneous evaluation of both BCS and morbidity on the rabbit farm is recommended for the right assessment of welfare conditions. In this study, the relationships between both variables have been shown, as well as how other intrinsic and extrinsic risk factors modulate these variables; and thus, these factors should be considered during a welfare assessment.