Animal welfare (AW) on 19 intensive dairy farms (DF) from the central zone of Chile was studied using Welfare Quality protocol (WQP); 18 were qualified between acceptable and enhanced, one as non-classified, and none as excellent. The objective of the present study was identify the specific problems of AW on these DF using the data on which the evaluations were made. WQP assesses AW on animal-based observations (cow or herd level) and on indirect information from farm records. For each observation or record, an average value/DF was obtained and compared with the alarm value (AV) for each indicator; AV is considered as the minimum value acceptable. For some indicators, AV was provided by WQP, otherwise this was calculated as 25% of the distance between maximum and minimum value found on the evaluation. Then the percentages of DF that exceeded the AV for each indicator were obtained and ranked to identify the principal problems. Problems were related to animal health, where 78.9, 52.6, 53, 40 and 40% of DF exceeded the AV on: % cows with areas of hairless patch, Total % of lame cows, % of cows with dystocia, mortality and downer cows, respectively; although some sanitary indicators as: % of cows with oral, nasal or vulvar secretions, as well % of cows with diarrhea did not show problems at all. Housing problems are mainly related to dirtiness (68.5, 57.9, 52.6% of DF had problems on: % of cows with udder dirty, % of cows with flank/upper leg dirty and % of cows with dirty lower legs, respectively). With regard to animal behavior, social interaction among cows did not seem to be a major problem; however, at human-cow interaction there is poor AW: 64.7 and 58.8% of DF showed problems with flight zone and % of cows that can be touched, respectively. Good feeding aspects did not appear as a major AW problem. The results show diverse aspects of management and housing, which affect the AW of dairy cows. This study has identified those problems that deserve greater attention in training of farm workers. Funded by project No. FOOD-CT-2004–506508 and CONICYT.