Diarrhea and respiratory disease are major health problems for dairy calves, often causing calf mortality. Previous studies have found calf mortality to be higher in organic dairy herds compared to conventional herds. The aim of this study was to investigate the association between production system (conventional/organic), season (summer/winter) and calf mortality risk, diarrhea, signs of respiratory disease and ocular discharge, respectively, for dairy heifer calves aged 0–180 days. Sixty Danish dairy herds, 30 conventional and 30 organic, were visited once during summer and once during winter. During the herd visits, calves were clinically examined for signs of diarrhea, hampered respiration, nasal discharge, coughing and ocular discharge. Data on mortality were obtained from the Danish Cattle Database. Data were analyzed using logistic regression models, with mortality risk and disease measures as outcome variables for each of three calf age groups: 0–28, 29–90 and 91–180 days. In organic herds, odds of mortality among calves aged 0–28 days were 2.09 (95% confidence interval (CI): 1.38–3.15) times higher during winter compared to summer. Odds of nasal discharge for calves 0-28 days in organic herds were 10.3 (95% CI: 2.27–46.6), 10.7 (95% CI: 2.40–40.0) and 5.97 (95% CI: 1.29–27.6) times higher for organic and conventional herds during winter (OW and CW) and conventional herds during summer (CS) respectively, compared to organic herds during summer (OS). For calves aged 29–90 days, odds of nasal discharge were 8.22 (95% CI: 3.88–17.4), 8.06 (95% CI: 3.18–20.4) and 2.86 (95% CI: 1.08–7.55) times higher for OW, CW and CS respectively, compared to OS. Odds of nasal discharge for calved aged 91–180 days were 7.03 (95% CI: 3.95–12.5) and 4.27 (95% CI: 1.81–10.1) times higher for OW and CW respectively compared to OS. For calves aged 29–90 days, odds of coughing were 2.23 (95% CI: 1.06–4.71) and 3.82 (95% CI: 1.76–8.21) times higher for OW and CW compared to OS, while odds of coughing for calves aged 91–180 days were 2.09 (95% CI: 1.19–3.67) and 2.55 (95% CI: 1.39.4.67) times higher for OW and CW compared to OS. Odds of ocular discharge for calves aged 29–90 days were 0.22 (95% CI: 0.10–0.52), 0.27 (95% CI: 0.11–0.66) and 0.42 (95% CI: 0.18–0.99) times higher for OW, CW and CS compared to OS. In conclusion, mortality and morbidity of Danish dairy heifer calves are, for some variables and in certain age groups, dependent on production system and season.