Isospora suis is a common pathogen in piggeries and one of the main causative agents of scours in suckling piglets. Besides specific treatment, optimised hygiene including chemical disinfection is considered essential in the control of isosporosis. The suitability of the cresol-based product Neopredisan 135-1® (NP) to inactivate oocysts in vitro and to reduce infection pressure in commercial piggeries was evaluated. Under in vitro conditions, NP at a final concentration of 2 or 4% induced lysis of more than 95% of sporulated oocysts at a contact time of 30 min and destroyed all oocysts after a contact time of 90 min or more. A total of six trials (T1–T6) were performed on two farms (I and II). T5 was split into two parts, T5/1 and T5/2. Two groups of litters kept in farrowing crates either disinfected conventionally before farrowing (controls, group C) or disinfected with 4% dilution of NP before farrowing and with 2% NP one to three times thereafter (group NP) were compared in each trial. Altogether, 81 litters were randomly allocated to group NP and 77 litters to group C (comprising a total of 1,465 piglets). Piglet faeces were collected individually 5 days after birth and six times thereafter in intervals of 2 or 3 days from four piglets per litter and microscopically examined for oocysts of I. suis. Diarrhoea scores, other clinical data (skin turgidity, coat length etc.), weights and loss of piglets until weaning were recorded. One trial (T3) could not be analysed because of insufficient cleaning before disinfection. In group C, litter prevalence of I. suis ranged between 40 and 80%. The proportion of positive litters was considerably reduced by approximately 50% in disinfected crates except for one trial, and the number of affected piglets decreased by up to 80%. Diarrhoea and oocyst excretion were significantly associated. Diarrhoea was less frequently observed in disinfected crates. In general, isosporosis appeared mild to subclinical, and no significant effects of disinfection on other clinical data, weight gain and number of weaned piglets were noted. It is concluded that NP efficiently inactivates oocysts of I. suis, and that additional disinfection after farrowing is suited to reduce infection pressure. No clear relation of infection prevalence to the frequency of intermediate disinfection (one, two or three times) was seen, and thus, single intermediate disinfection 1 week after farrowing is considered sufficient.