Pyrite (FeS2) from coal, sedimentary rocks, and hydrothermal ore deposits generally contains hazardous selenium (Se) and arsenic (As) that are released in natural waters through oxidative dissolution of the host. Knowing how As and Se are structurally incorporated into pyrite has important implication in controlling or preventing their release because trace metal(loid) substitution accelerates the dissolution of pyrite. Previous extended X-ray absorption fine structure (EXAFS) studies have reported that nominally monovalent arsenic clusters at the sulfur site forming As-As pairs at 3.2 Å, whereas monovalent Se does not form Se-Se pairs at this distance for unknown reason. Here, we revisit this question using As and Se K-edge X-ray absorption near-edge structure (XANES) and EXAFS spectroscopy complemented with atomistic calculations. We find that neither As nor Se atoms can be differentiated from S atom at 3.2-3.3 Å, the cluster and dilute model-fits to As-and Se-EXAFS data yielding equivalent least-squares solutions. Thermodynamic calculations of Fe48As3S93 (3.8 wt.% As) and Fe48Se3S93 (4.0 wt.% Se) structures show that the formation of As-As pairs is energetically favorable and the formation of Se-Se pairs unfavorable. Thus, the equilibrium distribution of As and Se predicted by calculation agrees with published EXAFS data. However, this agreement is incidental because EXAFS fits are ambiguous, the same EXAFS spectra being fit indifferently with a cluster and 2 a dilute model. Regarding Se, the dilute model-fit is probably correct since Se-Se pairs are precluded thermodynamically. The situation is less clear for As. The lowest energy atomic arrangement of As in Fe48S93As3 is similar to the local structure of As in arsenopyrite (FeAsS), thus supporting the cluster model. However, the energy gain to total energy provided by the formation of As clusters decreases with decreasing As concentration, making them thermodynamically less favorable below 1.0 wt.%. Determining the actual distribution pattern of As in pyrite is challenging.