The aim of this study was to identify possible risk factors for 1-90 day calf mortality in large Swedish dairy herds. Sixty herds with a herd size of ≥160 cows were visited once between December 2005 and March 2006. Thirty herds were known to have low mortality (LM) and 30 were known high mortality herds (HM). Upon the visit, data about housing and management was collected from interviews with personnel responsible for the calves. The herd status regarding the calves' passive transfer (total protein), levels of α-tocopherol, β-carotene and retinol, and excretion of faecal pathogens (Cryptosporidium spp., Escherichia coli F5, rota and corona virus) was evaluated based on targeted sampling of high risk calf groups; in each herd, blood and faecal samples were collected from calves 1-7 and 1-14 days old, respectively. Similarly, the herd status regarding clinical respiratory disease in calves and history of respiratory virus exposure was evaluated based on lung auscultations and blood samplings of calves 60-90 days old. The median calf mortality risk (in calves 1-90 days of age) among HM herds was 9% (Range: 6-24%) and among LM herds 1% (Range: 0-2%). LM and HM herds were compared using five logistic regression models, covering potential risk factors within different areas: "Disease susceptibility", "Factors affecting the gastrointestinal tract", "Factors related to transmission of infectious disease", "Hygiene" and "Labour management". The percentage of calves, 1-7 days old, with inadequate serum concentrations of α-tocopherol and β-carotene were significantly higher in HM herds compared to LM herds and also associated with higher odds of being a HM herd (OR=1.02; p=0.023 and OR=1.05; p=0.0028, respectively). The variable "Average number of faecal pathogens in the sampled target group" was significantly associated with higher odds of being a HM herd (OR=4.65; p=0.015), with a higher average in HM herds. The percentage of calves with diarrhoea treated with antibiotics was significantly higher in HM herds and was associated with higher odds of being a HM herd (OR=1.08; p=0.021). The median age at death of calves in the age interval 1-90 days that died during a one-year period was significantly lower among HM herds (13 days) than in LM herds (24 days) (p=0.0013) The results indicate that gastrointestinal disorders may be an important cause of calf mortality in large Swedish dairy herds. Furthermore, our study provides additional indications that fat soluble vitamins might play an important role for calf health.