Milk yield, milk ingredients, health and other, production-related parameters of subclinically infected, Mycobacterium avium ssp. paratuberculosis (MAP-) shedding (positive faecal PCR, n = 20) and non-shedding (negative faecal PCR, n = 10) dairy cows were compared in the period from 10 days prepartum to 120 days postpartum. Body condition, rumen fill and faeces scores were lower in the MAP-shedding cows. There was no significant difference in plasma or urine metabolic parameters between the groups. Milk yield and lactose content tended to be lower (P = 0.074 and 0.077, respectively), somatic cell count tended to be higher (P = 0.097), while milk fat content was significantly higher (P = 0.006) in MAP-shedding cows than in the controls. Milk protein content did not differ between the groups. All other health and production parameters [number of reproductive tract treatments, number of udder treatments, number of artificial inseminations (AIs), calving interval, and service period] were significantly better in the control group. It is concluded that MAP infection, even in a subclinical form, has a significant impact on some production and health parameters of dairy cows.