Animal welfare is of increasing public interest, and the pig industry in particular is subject to much attention. The aim of this study was to identify and compare areas of animal welfare concern for commercial pigs in four different production stages: (1) gestating sows and gilts; (2) lactating sows; (3) piglets; and (4) weaner-to-finisher pigs. One welfare assessment protocol was developed for each stage, comprising of between 20 and 29 animal welfare measures including resource-, management- and animal-based ones. Twenty-one Danish farms were visited once between January 2015 and February 2016 in a cross-sectional design. Experts (n = 26; advisors, scientists and animal welfare controllers) assessed the severity of the outcome measures. This was combined with the on-farm prevalence of each measure and the outcome was used to calculate areas of concern, defined as measures where the median of all farms fell below the value defined as ‘acceptable welfare.’ Between five and seven areas of concern were identified for each production stage. With the exception of carpal lesions in piglets, all areas of concern were resource- and management-based and mainly related to housing, with inadequate available space and the floor type in the resting area being overall concerns across all production stages. This means that animal-based measures were largely unaffected by perceived deficits in resource-based measures. Great variation existed for the majority of measures identified as areas of concern, demonstrating that achieving a high welfare score is possible in the Danish system.