We generalize the seminal polynomial partitioning theorems of Guth and Katz to a set of semi-Pfaffian sets. Specifically, given a set of -dimensional semi-Pfaffian sets, where each is defined by a fixed number of Pfaffian functions, and each Pfaffian function is in turn defined with respect to a Pfaffian chain of length , for any , we prove the existence of a polynomial of degree at most such that each connected component of intersects at most elements of . Also, under some mild conditions on , for any , we prove the existence of a Pfaffian function of degree at most defined with respect to , such that each connected component of intersects at most elements of . To do so, given a -dimensional semi-Pfaffian set , and a polynomial of degree at most , we establish a uniform bound on the number of connected components of that intersects; that is, we prove that the number of connected components of is at most . Finally as applications, we derive Pfaffian versions of Szemerédi-Trotter type theorems, and also prove bounds on the number of joints between Pfaffian curves.

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