Atypical porcine pestivirus (APPV) has recently been reported to be associated with congenital tremor in newborn piglets. Only limited information is available about the prevalence at herd level in endemically infected herds. Therefore, the aim of this study was to determine the within-herd prevalence of APPV in a sub-clinically infected sow herd in Switzerland and to analyse associations between the serological status as well as the age and sex of the pigs, litter number and days after the last insemination. In a census sampling, blood was collected from 125 sows, aged 180 days or older, and six boars. Sera were examined applying an indirect APPV-specific ELISA to individual sera and an APPV RT-PCR targeting the NS3 encoding regions of APPV to pools of five. The APPV antibody status was classified into low (S/P value ≤ 0.5), intermediate (S/P value = 0.5-1) and high reactivity (S/P value > 1.0). None of the pooled serum samples was positive for specific genome fragments of APPV. Of the 131 samples, 53.4% were highly reactive, 39.7% showed an intermediate reactivity, and 6.9% showed a low reactivity in the indirect ELISA, that is, were serologically negative. Significant associations between the S/P values and the age of the pigs (p < .001), the litter number (p < .001) and the numbers of days after the last insemination (p = .0188) were observed. The results indicate that this sow herd was previously infected with APPV, while viremia was not detected in any of the adult pigs. This might explain the absence of clinical signs in the suckling pigs. Potential reinfection and circulation of APPV in this sow herd might be due to semen from commercial boar studs or APPV-positive animals in the absence of specific clinical signs.