Clusters of round objects (e.g., lotus seedpods) induce strong discomfort (trypophobic discomfort). A previous study has shown that trypophobic discomfort stems not only from middle but also low spatial frequency information, which should be rapidly transmitted to the amygdala via the superior colliculus and pulvinar pathway. Based on this finding, we hypothesized that trypophobic discomfort would be evoked by invisible trypophobic images; the present study examined this using a backward masking technique. We found that trypophobic images were reported as unpleasant significantly above the chance level irrespectively of visibility of the image (Experiments 1 and 2). On the other hand, detection sensitivity for trypophobic images was lower than that for neutral images (Experiment 3). Taken together, our findings suggest that emotional information about trypophobic objects is processed unconsciously although this information does not promote detection.