Malignant pleural mesothelial cells are affected by the extracellular milieu while such data on benign cells are scarce. Benign cells sense the extracellular environment with the Primary Cilium (PC) and its molecular complex, the BBSome, is critical for this process. Here we aimed at assessing the changes in BBSome genes expression in ordinary 2D and spheroid 3D cell cultures after incubation with pleural effusion fluids (PF) of several etiologies. Benign human mesothelial cells MeT-5A were incubated with PF from patients with mesothelioma (Meso-PF), breast cancer (BrCa-PF), hemothorax (Hemo-PF) and congestive heart failure (CHF-PF). Gene expression of BBS1, 2, 4, 5, 7, 9, 18 was assessed by quantitative real-time PCR (qRT-PCR) to monitor PF-induced gene expression changes. MeT-5A cell migration using the PC-modulating drugs ammonium sulfate (AS) and lithium chloride (LC) during PF incubation was also determined. BBSome gene expression upon influence of BrCa-PF and Hemo-PF was more pronounced in 2D compared to 3D, inducing global changes in 2D. CHF-PF and Meso-PF also induced changes in 2D but not as many, while in all cases MeT-5A grown in 3D were more resistant to the effects of the PF. Meso-PF decreased 2D cell migration, while the disturbance of PC in all PF cases resulted in decreased cell migration. These data suggest distinct BBSome molecular profile changes in benign mesothelial cells exposed to malignant and benign PF, in each case, in both 2D and 3D. Cell migration is sensitive to drug disturbance with PC modulators in PF-exposed cells.