Purpose To compare the diurnal efficacy and action on peak intraocular pressures (IOP) of 0.005% latanoprost and 0.5% timolol as primary therapy in 60 eyes having dark brown irides with primary open angle glaucoma (POAG). Methods A prospective, comparative, observer-masked, crossover, interventional trial including the mean of both eyes of 30 patients with POAG who were randomly started on either latanoprost once daily or timolol twice daily. Three months after treatment with one drug, the second drug was substituted. A masked observer carried out diurnal assessments of IOP before the start of therapy and at 3 and 7 months. The fourth month was the washout period for the first drug. Results The average baseline IOP was 23.36 ± 2.14 mm Hg, which was reduced by 8.8 ± 2.2 mmHg with latanoprost (p<0.01) and by 6.75 ± 1.9 mm Hg with timolol (p=0.01). The reduction was greater for latanoprost (p<0.005). The average peak IOP at baseline was 27.6 ± 2.22 mmHg. The effective fall in IOP at the time of new peaks in subsequent diurnal recordings of IOP compared to the baseline diurnal curve was 8.9 mm Hg with latanoprost (p<0.005) and 5.77 mm Hg with timolol (p<0.01). This difference in IOP reduction between the two drugs was statistically significant (p<0.01). Latanoprost had a lower efficacy in peak IOP reduction in eyes with evening peak of IOP than in those with morning peak (p<0.005). The efficacy of timolol was lower overall compared to latanoprost, but was similar in all circadian rhythms. The shift in timing of IOP peak was greater with latanoprost compared to timolol (4.34 hours vs –0.72 hours, p<0.01). A total of 90% of patients on latanoprost and 33.3% on timolol achieved a reduction of >30% in baseline mean IOP. The average of the trough IOP recorded in each of the individual baseline IOP curves was 19.05 ± 2.05 mm Hg. Conclusions Greater mean and peak IOP reduction was achieved with latanoprost compared to timolol. Dampening of the circadian rhythm was better with latanoprost. Latanoprost appears to be more effective than timolol at all points in time with greater efficacy in eyes with morning peaks compared to evening peaks.