Consider a repeated measurement regression model y ij = g ( x i ) + ε ij where i = 1 , … , n , j = 1 , … , m , y ij 's are responses, g ( · ) is an unknown function, x i 's are design points, ε ij 's are random errors with a one-way error component structure, i.e. ε ij = μ i + ν ij , μ i and ν ij 's are i.i.d random variables with mean zero, variance σ μ 2 and σ ν 2 , respectively. This paper focuses on estimating σ μ 2 and σ ν 2 . It is well known that although the residual-based estimator of σ ν 2 works very well the residual-based estimator of σ μ 2 works poorly, especially when the sample size is small. We here propose a difference-based estimation and show the resulted estimator of σ μ 2 performs much better than the residual-based one. In addition, we show the difference-based estimator of σ ν 2 is equal to the residual-based one. This explains why the residual-based estimator of σ ν 2 works very well even when the sample size is small. Another advantage of the difference-based estimation is that it does not need to estimate the unknown function g ( · ) . The asymptotic normalities of the difference-based estimators are established.