Broiler chicks usually hatch in the hatchery without access to feed and water until placement at the farm. This can affect their health and welfare negatively. Therefore, alternative strategies have been developed, for instance providing chicks with early nutrition in the hatchery or hatching eggs directly on-farm. However, information on the physical and mental welfare of chicks hatched in these systems compared to conventionally hatched chicks is limited. The aim of this study was to investigate the effects of alternative hatching systems on the welfare of broiler chickens in early and later life. A system comparison was performed with chickens that hatched conventionally in a hatchery (HH), in a system which provided light, feed, and water in a hatcher (hatchery-fed, HF), or on-farm (on-farm hatched, OH, where feed and water were available and transport of day-old chicks from the hatchery to the farm was not necessary). Chickens were reared in 3 batches, in 12 floor pens per batch (approximately 1,155 animals per pen), with a total of 12 replicates per treatment. Animal-based welfare indicators were assessed following standard protocols: plumage cleanliness, footpad dermatitis (FPD), hock burn, skin lesions (all at day 21 and 35 of age), and gait score (day 35). Furthermore, a set of behavioral tests was carried out: novel environment (day 1 and 21), tonic immobility, novel object, and avoidance distance test (day 4 and 35). Plumage cleanliness, hock burn, and skin lesions were affected by age but not by hatching system, with older broilers scoring worse than younger ones (P < 0.05). An effect of hatching system was only found for FPD, with the highest prevalence in HH chickens, followed by HF and OH chickens (P < 0.05). All responses measured in the behavioral tests were affected by age but not by hatching system. In later life, chickens were significantly less fearful than during the first days of life. The results indicate that conventionally hatched chickens scored significantly worse for FPD, whereas, in general, hatching system seemed to have minor effects on other broiler welfare indicators.