The objectives were to evaluate effects of high mastitis and ketosis risks (MRisk and KRisk) on commencement of luteal activity (CLA), luteal and follicular phase (LP and FP) lengths and cumulative pregnancy at 120 DIM (P/120) using data from an in-line milk analysis system (Herd Navigator, DeLaval). Starting at ~5 DIM and repeating every ~2d, L-lactate dehydrogenase and β-hydroxybutyrate were quantified by the system to generate MRisk and KRisk indicators (0–100%) based on a bio-model that accounted for individual cow variation in values. Milk progesterone (mP4) measures started at ~20 DIM. Records (n = 328,649) of 910 Holstein cows (2,278 lactations) were obtained from 4 Alberta herds. As indicators of potential clinical cases, only MRisk ≥ 70% and KRisk ≥ 90% were considered. Data of mP4 was used to determine CLA (first mP4 ≥ 5ng/mL), lengths of LP (period of mP4 ≥ 5ng/mL) and FP (period of mP4 < 5ng/mL between consecutives LP) and pregnancy (uninterrupted LP at ≥ 50d after AI). Effects of MRisk and KRisk on LP and FP lengths were evaluated on 2,891 cycles, while CLA and P/120 were evaluated on 1,823 lactations. Analyses used PROC GLIMMIX of SAS including parity, milk yield and DIM in the models. Incidences of MRisk and KRisk were 22.2 and 3.6% and occurred at (μ ± SD) 106 ± 56 and 36 ± 10 DIM. Overall LP and FP lengths (μ ± SEM) were 14.1 ± 0.2 and 13.9 ± 0.2d, and P/120 was 38% (range 30–51% among farms). The odds of having MRisk was increased (odds ratio [OR] = 5.5) in multiparous than in primiparous cows. The odds of MRisk was greater (OR = 3.8) in cows yielding ≥ 31kg/d than in those yielding < 31kg/d. MRisk did not affect CLA, but increased the occurrence of LP ≥ 16d (OR = 4.4) and FP ≥ 12d (OR = 1.5). MRisk during first 120 DIM decreased P/120 (OR = 0.5). The occurrence of KRisk tended (P = 0.09) to be greater in multiparous than in primiparous cows (OR = 8.9), but did not affect reproductive parameters. Cows experiencing high mastitis risk were more likely to have abnormal (i.e., prolonged) luteal and follicular phases during estrous cycles, and less likely to be pregnant at 120 DIM.