Reports that low‐intensity microwave radiation induces heat‐shock reporter gene expression in the nematode, Caenorhabditis elegans, have recently been reinterpreted as a subtle thermal effect caused by slight heating. This study used a microwave exposure system (1.0 GHz, 0.5 W power input; SAR 0.9–3 mW kg−1 for 6‐well plates) that minimises temperature differentials between sham and exposed conditions (≤0.1 °C). Parallel measurement and simulation studies of SAR distribution within this exposure system are presented. We compared five Affymetrix gene arrays of pooled triplicate RNA populations from sham‐exposed L4/adult worms against five gene arrays of pooled RNA from microwave‐exposed worms (taken from the same source population in each run). No genes showed consistent expression changes across all five comparisons, and all expression changes appeared modest after normalisation (≤40% up‐ or down‐regulated). The number of statistically significant differences in gene expression (846) was less than the false‐positive rate expected by chance (1131). We conclude that the pattern of gene expression in L4/adult C. elegans is substantially unaffected by low‐intensity microwave radiation; the minor changes observed in this study could well be false positives. As a positive control, we compared RNA samples from N2 worms subjected to a mild heat‐shock treatment (30 °C) against controls at 26 °C (two gene arrays per condition). As expected, heat‐shock genes are strongly up‐regulated at 30 °C, particularly an hsp‐70 family member (C12C8.1) and hsp‐16.2. Under these heat‐shock conditions, we confirmed that an hsp‐16.2::GFP transgene was strongly up‐regulated, whereas two non‐heat‐inducible transgenes (daf‐16::GFP; cyp‐34A9::GFP) showed little change in expression. Bioelectromagnetics 30:602–612, 2009. © 2009 Wiley‐Liss, Inc.