\iftoggle endauthorlist We report results of a deep all-sky search for periodic gravitational waves from isolated neutron stars in data from the S6 LIGO science run . The search was possible thanks to the computing power provided by the volunteers of the Einstein @ Home distributed computing project . We find no significant signal candidate and set the most stringent upper limits to date on the amplitude of gravitational wave signals from the target population . At the frequency of best strain sensitivity , between 170.5 and 171 Hz we set a 90 % confidence upper limit of 5.5 \times 10 ^ { -25 } , while at the high end of our frequency range , around 505 Hz , we achieve upper limits \simeq { 10 } ^ { -24 } . At 230 Hz we can exclude sources with ellipticities greater than 10 ^ { -6 } within 100 pc of Earth with fiducial value of the principal moment of inertia of 10 ^ { 38 } \textrm { kg m } ^ { 2 } . If we assume a higher ( lower ) gravitational wave spindown we constrain farther ( closer ) objects to higher ( lower ) ellipticities .