Cytokines are physiological seminal components and their abnormal levels, reported in different pathological conditions, negatively influence the sperm function. We analysed the relationship between interleukin (IL)-6 and IL-33 levels and lipid peroxidation (LPO), measured both in semen and sperm lysate, in 44 human semen samples. The semen analysis was performed following the WHO guidelines. Seminal IL-6 and IL-33 concentrations were assessed by ELISA and LPO was evaluated measuring malondialdehyde (MDA) both in seminal plasma and viable spermatozoa. Two small groups of patients with varicocele and infection were extrapolated from the cases analysed and the variables compared with those of a group of control. IL-33 levels were undetectable in all samples and IL-6 levels were positively correlated with both seminal and sperm MDA concentrations (p < 0.01) and negatively with sperm parameters (p < 0.01). Seminal and sperm MDA levels were both negatively correlated with sperm parameters (p < 0.01). IL-6 and semen MDA showed an exponential positive relationship, whereas MDA values measured in viable spermatozoa were low until IL-6 amount reached a concentration of >30 pg/mL, rising consistently. By comparing the variables in the groups, we confirmed that a high IL-6 concentration in the varicocele and infection groups was concomitant with an increase of seminal MDA levels, but also with MDA measured in viable spermatozoa, which represents the novelty of this study. We identified the IL-6 threshold, beyond which sperm MDA concentration rises concomitantly with the increase of IL-6 concentration. Other studies are needed, considering the increasing number of patients with different pathologies affecting male infertility.