A new expression for the variance of scalar frequency functions estimated using the least-squares method is presented. The expression is valid for finite sample size and for a class of model structures, which includes finite impulse response, Laguerre and Kautz models, when the number of estimated parameters coincides with the number of excitation frequencies of the input. The expression gives direct insight into how excitation frequencies and amplitudes affect the accuracy of frequency function estimates. The relevance of the expression when more excitation frequencies are used is also discussed.