The objective of this study was to evaluate the effect of two Swiss animal welfare friendly housing programs, 'regular access to outdoor facilities' (RAUS) and 'improved loose housing systems' (BTS) on health and welfare of dairy cows. During two years, the following indicators of health and welfare were observed on 136 randomly selected dairy farms: injuries around the joints, callosities, lameness, teat injuries, cleanliness, behaviour during lying and rising, body condition score, and incidence of medical treatments. Farms participating in both housing programs (BTS + RAUS) and farms with the program RAUS were compared to traditional farms that did not participate in a program. Housing system and management practice were recorded as additional factors influencing health and welfare of cows. Cows on farms participating in BTS + RAUS had, on average, fewer injuries around the hocks and fewer callosities at the carpal joints than cows in farms which did not participate in a housing program. Lameness was most frequent in cows of farms without housing program, followed by cows in tie stalls with the program RAUS and cows in loose housing systems with BTS + RAUS. There were fewer antibiotic treatments in farms with BTS + RAUS compared to the other farms.