Clear cell renal cell carcinoma (ccRCC) is the most common and aggressive subtype of kidney cancer, with high mortality rates worldwide. The sonic hedgehog (SHH) molecular cascade is altered in various malignancies in tumorigenesis, and several SHH pathway inhibitors have been considered as potential anticancer drugs. The aim of the present study was to determine the expression profile of SHH signaling components and their target genes in ccRCC. Additionally, the present study examined the effects of SHH pathway inhibitory drugs (RU-SKI43, cyclopamine and GLI-antagonist 61) on cell viability, cell cycle progression, expression levels of SHH target genes and migration ability in 786-O, ACHN and HK2 cells. The study also included paired tumor and normal samples from 62 patients with ccRCC. The mRNA levels in clinical samples and cell lines were measured via reverse transcription-quantitative PCR. Cell viability was examined using a sulforhodamine B assay. Flow cytometry was used to investigate cell cycle progression and the migratory rate of cells was assessed using a wound healing assay. High mRNA levels of
SHH
, smoothened (
SMO
), glioma-associated zinc finger protein (
GLI
)
1-3
, BCL2 apoptosis regulator (
BCL2
), MYC proto-oncogene (
MYC
), vascular endothelial growth factor A (
VEGFA
) and cyclin D1 (
CCND1
) were observed in the tumor tissues, especially in early ccRCC, according to the TNM stage or World Health Organization/International Society of Urological Pathology (ISUP) grade. High expression levels of
VEGFA
, as well as low
CCND1
mRNA expression, were associated with short overall survival, and increased
VEGFA
expression was an independent prognostic factor of a poor outcome in patients with advanced ISUP grade (Cox hazard ratio test). Cyclopamine treatment was found to arrest 786-O cells in the G
2
/M phase and decreased the expression levels of
GLI1
,
BCL2
,
VEGFA
and
CCND1
. RU-SKI43 inhibited cell migration and decreased the expression levels of
BCL2
,
MYC
and
CCND1
in ACHN cells. Overall, the results of the present study suggested that SHH signaling may be involved in the early development of ccRCC, and the expression levels of
CCND1
and
VEGFA
may serve as prognostic factors of this disease. Cyclopamine and RU-SKI43 appear to be potential anti-renal cell carcinoma drugs; however, this hypothesis requires verification by further
in vivo
studies.