The objective was to compare the relationships between luteal activity and fertility, and relate these parameters to metabolic indices and body condition changes in multiparous Estonian Holstein cows on two commercial dairy farms under different management and levels of production and nutrition (higher, H, n=54 (71 lactations) and lower, L, n=39 (39 lactations)). For statistical analysis cows were categorized according to their milk progesterone (P4) profiles as follows: normal ovarian function; delayed start of cyclicity (DC) (interval from calving to first luteal response (P4⩾5 ng/ml up to and more than 50 d respectively, followed by regular cyclicity); cessation of luteal activity (prolonged interluteal interval, P4<5 ng/ml, with a duration of ⩾14 d between two adjacent luteal phases); prolonged luteal activity (P4 levels ⩾5 ng/ml for ⩾20 d without preceding insemination). The Mixed procedure of the SAS system was used to compare milk production traits, blood metabolites (ketone bodies, non-esterified fatty acids, total cholesterol) and aspartate aminotransferase, body condition scores (BCS) and fertility parameters between the two farms, and also fertility parameters between the farms within P4 categories. Differences in milk fat/protein ratio, ketone body levels and BCS indicated a deeper negative energy balance (NEB) during the first month after calving on farm L. On both farms nearly 50% of the recently calved dairy cows suffered from ovarian dysfunction during the post-partum period. Delayed start of cyclicity was the most prevalent abnormal P4 profile, 25% and 28% on farms H and L, respectively. Prolonged luteal activity accounted for one-third of atypical ovarian patterns on farm H, and cessation of luteal activity on farm L. On farm L, DC cows had lower BCS values from day 10 to day 90 after calving compared with normal cows (P<0·01) and cows lost more BCS (1·2 units) during the 40 d after calving than normal resumption cows (0·75 units; P<0·05). On farm H with moderate NEB the delayed start of ovulation post partum did not impair subsequent reproductive performance.