Purpose To assess if there are differences in the structure-function associations between healthy and glaucomatous eyes. Methods Structure-function associations were assessed in healthy and glaucomatous eyes in three datasets, globally and in the six sectors of the optic nerve head. Structural parameters included rim area (RA) and retinal nerve fiber layer thickness (RNFLT). Functional parameters included unweighted mean of sensitivity thresholds (MS) and unweighted mean of total deviation values (MD), assessed with standard automated perimetry, short-wavelength automated perimetry, frequency-doubling technology perimetry, or contrast sensitivity perimetry. All structural and functional parameters were expressed as percent of mean normal. SF associations were assessed with correlation analyses (Pearson, Spearman and Kendall). We also assessed the SF associations with linear regression analyses: the generalized estimating equation (GEE) was used to adjust for inter-eye correlations and ordinary least squares (OLS) linear models were used when these adjustments were not necessary. We applied Bonferroni corrections to adjust for the impact of multiple comparisons. Results Overall, none of the Pearson correlations tested in healthy eyes were significant (correlations ranged from -0.17 to 0.37), whereas 77% of the correlations tested in glaucomatous eyes were significant (correlations ranged from 0.01 to 0.79). Similarly, none of the slopes obtained with GEE and OLS were significant in healthy eyes (slopes ranged from -0.30 to 0.87), whereas 82% of the slopes obtained in glaucomatous eyes were significant (slopes ranged from 0.02 to 1.38). Conclusions Significant associations between structure and function were consistently observed in glaucomatous eyes, but not in healthy eyes. These differences in association should be considered in the design of structure-function models for progression.