The G protein‐coupled receptors, GPR41 and GPR43, are activated by short‐chain fatty acids (SCFAs), with distinct rank order potencies. This study investigated the possibility that SCFAs modulate intestinal motility via these receptors. Luminal SCFA concentrations within the rat intestine were greatest in the caecum (c. 115 mmol L⁻¹) and proximal colon. Using similar concentrations (0.1–100 mmol L⁻¹), SCFAs were found to inhibit electrically evoked, neuronally mediated contractions of rat distal colon, possibly via a prejunctional site of action; this activity was independent of the presence or absence of the mucosa. By contrast, SCFAs reduced the amplitude but also reduced the threshold and increased the frequency of peristaltic contractions in guinea‐pig terminal ileum. In each model, the rank‐order of activity was acetate (C2) ≈ propionate (C3) ≈ butyrate (C4) > pentanoate (C5) ∼ formate (C1), consistent with activity at the GPR43 receptor. GPR43 mRNA was expressed throughout the rat gut, with highest levels in the colon. However, the ability of SCFAs to inhibit neuronally mediated contractions of the colon was similar in tissues from wild‐type and GPR43 gene knockout mice, with identical rank‐orders of potency. In conclusion, SCFAs can modulate intestinal motility, but these effects can be independent of the GPR43 receptor.