Background Modern persistent organic pollutants (POPs) contamination are logical candidates in the investigation of the, as yet, unexplained association between allergic disease and progressive industrialisation. POPs have been detected in human cord blood, placental tissues and breast milk, and the reported association between cord blood IgE levels and cord/placental POP levels has raised concerns about potential immunological effects in early life. Methods The initial aim of this study was to determine if POPs were detectable in maternal blood, cord blood, placental tissues, adipose tissue and breast milk samples from randomly selected Western Australian women ( n = 31), where allergic disease is epidemic. Gas chromatography was used to detect polychlorinated biphenyl compounds [PCBs] (as Aroclor 1232, 1254, 1260) and organochlorine (OC) pesticides, including p, p′-DDT, p, p′-DDE, hexachlorobenzene (HCB), lindane, heptachlor epoxide, dieldrin and chlordane. Secondly, we assessed the relationship between POP levels detected in vivo and maternal and neonatal responses (cytokine and lymphoproliferation) to allergens and mitogens. Results Low level POP contamination was detected in adipose tissue and breast milk (but not in cord blood, maternal blood or placental tissues). The most ubiquitous compound found in over 90% of adipose tissues samples was a OC metabolite of DDT, p, p′-DDE (median 0.07 mg/kg; interquartile range [IQR] 0.05–0.12). However, the majority of other OC compounds were not detectable and PCB were not detectable in any samples. The three main residues detected in breast milk were p, p′-DDE (0.003 mg/l; 0.001–0.009), dieldrin (0.001 mg/l; 0.001–0.046) and HCB (0.001 mg/l; 0.001–0.001). These levels are significantly lower than reported over 20 years ago. There were no consistent relationships between POP levels in vivo and maternal or infant responses, with the exception of a significant inverse association (Spearman rank correlation: r = −0.406, p = 0.049) between maternal adipose tissue levels of OC p, p′-DDE and maternal T helper cell Type 1 interferon [IFN] γ to mitogens. Conclusion This study provides the first evidence (in Australia) since the early 1990’s that adipose OC levels have continued to fall. The negligible levels in this randomly selected group are significantly lower than those previously recorded, suggesting that POP contamination (at biologically relevant levels) is not likely to be a major contributing factor in the increasing rates of allergy in Western Australia. However, the relationship between Th1 immune function and OC contamination is consistent with other reports and is worth investigating as a relevant factor in populations where OC contamination is greater.