In Italy, pig breeding is characterised by intensive farms in which parasitic diseases often present a subclinical pattern, while being responsible for decreased animal welfare and great economic losses. The present study aimed to assess the prevalence of major parasites in pigs, and, for this purpose, 880 faecal samples of fattening pigs raised in 22 intensive farms located in northern Italy were collected in two different sampling sessions, at the beginning and end of the fattening cycle. For the detection of helminth eggs and coccidian oocysts, a quantitative flotation technique was used, whereas a conventional PCR was performed to confirm the identification of cestode eggs found by copromicroscopic analysis. Moreover, data regarding herd management were collected to assess risk factors for parasite occurrence. A total of 95 samples were positive for at least one parasitic taxon (10.8%); the most detected parasite was Ascaris suum (7.6%), followed by Trichuris suis (1.7%) and Cystoisospora suis (0.9%). Further, eggs with morphometric features compatible with those of Hymenolepis diminuta were detected in 16 samples (1.8%), and the analysis of sequences confirmed the identification of cestode eggs. Statistical analysis showed that large farms and those applying the all-in/all-out system were associated with a lower risk of nematode infection. This study provided data on prevalence and burden of gastrointestinal parasites in two different times of the fattening cycle. It was evidenced that endoparasites are persistent, albeit with low prevalences, and would need specific measures to reduce their effects on both animal health and productivity.