Disclosed are a method and system for estimating the skew and offset between two clocks in a computer system. The method comprises the steps of obtaining a first set of data values representing a forward delay between the first and second clocks, and obtaining a second set of data values representing a negative backward delay between the first and second clocks. The method comprises the further steps of forming a lower convex hull for said first set of data values, and forming an upper convex hull, above the lower convex hull, for said second set of data values. The clock offset and the skew between said first and second clocks are estimated using those convex hulls. In a preferred embodiment, this estimation is made by identifying a best clock line between the first and second convex hulls.