In this article, we focus on the influence of side groups on terminal alkyne creation, in aliphatic polymers submitted to swift heavy ions, under vacuum. Terminal alkyne creation was compared in polyethylene and in substituted polymers. We selected two classes of side groups: alkyl groups, which differed in their length (polypropylene and polybutene) and allyl groups, which were linear (EPDMh) or cyclic (EPDMn). Irradiated samples were analyzed using Fourier transform IR spectroscopy, in the transmission mode, at room temperature. Alkynes are created when the electronic stopping power, (dE/dx)e, exceeds a threshold value. This threshold value was moderately influenced by the presence of an alkyl side chain but was clearly reduced in the presence of C=C bonds on the side chain. Nevertheless, in all-saturated polymers, below the (dE/dx)e threshold, terminal alkyne formation is observed after a latent dose, rather independently of the side-chain length and directly related to the formation of radiation-induced double bonds prior to alkyne formation. Under S ion irradiation, the radiation chemical yield G0 value obtained in EPDMh was 4 times the value of G0 in PE. This effect is understandable only if important energy transfers, from the backbone to C=C double bonds, are considered.