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Blood samples were collected between 2012 and 2014 on 16 small one-site pig farms with 34 to 79 breeding animals. 1636 serum samples of breeding animals and 815 serum samples of fatteners were tested with IDEXX PRRS ELISA. 1054 samples (from 7 small farms) were screened with one step RT-PCR (Qiagen, Germany) using sequences based on the open reading frame 7 (ORF7), which detect Type 1 and Type 2 PRRSV strains respectively. 81 serum samples of breeding animals and 85 serum samples of fatteners were tested with Swine Salmonella Antibody Test Kit (IDEXX) and CHEKIT*APP-ApxIV (IDEXX). 80 serum samples of sows were assayed for leptospira antibody using a microscopic agglutination test (MAT). Antibodies against porcine reproductive and respiratory virus (PRRSV) were detected in 67.5% of breeding animals and in 41.1% fatteners. By RT-PCR, PRRSV was detected in 7.9% of serum samples. The seroprevalence to salmonella in breeding animals was 21% and in fatteners 5.8%. The prevalence against Actinobacillus pleuropneumoniae (APP) antibodies was 87.6% in breeding animals and 49.4% in fatteners. Three farms were positive to leptospirosis (serovar hardjo, serovar grippotyphosa). We suggested farms free of PRRS to continue with biosecurity practices and 11 farms with PRRS we had suggested biosecurity measures and herd closure. Almost all breeding animals had antibodies against APP, though clinical signs were not present. Seroprevalence of salmonella in Slovenia is low. 3 pig farms had leptospirosis. All tree farms treated infected pigs.