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Abstract Background To gain more insight in whether failure of intrauterine insemination (IUI) treatment in patients with idiopathic subfertility could be related to diminished fertilization, the aim of this study is to compare the fertilization of an initial IVF procedure after six cycles of IUI and the fertilization of an initial IVF procedure without preceding IUI cycles in couples with idiopathic subfertility. Methods We performed a complimentary analysis of a randomized controlled trial, in which the number of total fertilization failure (TFF) in the first IVF procedure after unsuccessful IUI was compared to those of IVF without preceding IUI in patients with idiopathic subfertility. These patients participated in a previous study that assessed the cost effectiveness of IUI versus IVF in idiopathic subfertility and were randomized to either IUI or IVF treatment. Results 45 patients underwent IVF after 6 cycles of unsuccessful IUI and 58 patients underwent IVF immediately without preceding IUI. In 7 patients the IVF treatment was cancelled before ovum pick. In the IVF after unsuccessful IUI group TFF was seen in 2 of the 39 patients (5%) versus 7 of the 56 patients (13%) in the immediate IVF group. After correction for confounding factors the TFF rate was not significantly different between the two groups (p = 0.08, OR 7.4; 95% CI: 0.5–14.9). Conclusion Our data showed that TFF and the fertilization rate in the first IVF treatment were not significantly different between couples with idiopathic subfertility undergoing IVF after failure of IUI versus those couples undergoing IVF immediately without prior IUI treatment. Apparently, impaired fertilization does not play a significant role in the success rate of IUI in patients with idiopathic subfertility.