Abstract: The rare decays B-s,d(0) -> l(+)l(-) are analyzed within the general framework of the aligned two-Higgs doublet model. We present a complete one-loop calculation of the relevant short-distance Wilson coefficients, giving a detailed technical summary of our results and comparing them with previous calculations performed in particular limits or approximations. We investigate the impact of various model parameters on the branching ratios and study the phenomenological constraints imposed by present data.