This paper considers a modification of generalized estimating equations (GE
E) for handling missing binary response data. The proposed method uses Gaus
sian estimation of the correlation parameters. i.e., the estimating functio
n that yields an estimate of the correlation parameters is obtained from th
e multivariate normal likelihood. The proposed method yields consistent est
imates of the regression parameters when data are missing completely at ran
dom (MCAR). However, when data are missing at random (MAR), consistency may
not hold. In a simulation study with repeated binary outcomes that are mis
sing at random, the magnitude of the potential bias that can arise is exami
ned. The results of the simulation study indicate that, when the working co
rrelation matrix is correctly specified, the bias is almost negligible for
the modified GEE. In the simulation study, the proposed modification of GEE
is also compared to the standard GEE. multiple imputation, and weighted es
timating equations approaches. Finally, the proposed method is illustrated
using data from a longitudinal clinical trial comparing two therapeutic tre
atments, zidovudine (AZT) and didanosine (ddI), in patients with HIV.