Rotaviruses (RVs) are an important cause of piglet diarrhea. This study aimed to determine the prevalence of rotavirus A, B, and C (RVA, RVB and RVC) in two RVA-vaccinated (VAC) and four non-vaccinated (NON-VAC) farms, and the impact of RVA vaccination on production parameters. Additionally, RVs prevalence in consecutive weekly groups from one vaccinated and one non-vaccinated farm was assessed. Diarrheic feces or ileum content were screened for RVs using real-time RT-PCR. In VAC, no RVA or RVB was detected, while RVC was found in all the samples (15/15). In NON-VAC, RVA, RVB, and RVC were detected in 10.5%, 13.2%, and 52.6% of samples, respectively. RVC was the most prevalent species in longitudinal study, while RVA was found in single samples. RVB was detected in one sample from the vaccinated farm, and in four out of five groups from the non-vaccinated farm. The pre-wean mortality and weaning weight were lower in the vaccinated than in the non-vaccinated farm. Low RVA prevalence and no noticeable improvement in weaning outcomes suggest vaccination was probably unjustified. Our study emphasizes the importance of comprehensive screening before and after vaccination and highlights the importance of including RVB and RVC in diagnostics of neonatal diarrhea.