Here's a modified snippet of my answer linked in a comment. Function returns the window object of an (i)frame with id passed (id), or null, if the (i)frame is not found. This method works only, if all the (i)frames are in the same domain. Also ids given to (i)frame elements must be unique throughout all documents involved in the window structure.
function searchFrame(id) { // id = the id of the wanted (i)frame
var result = null, // Stores the result
search = function (iframes) { // Recursively called function
var n; // General loop counter
for (n = 0; n < iframes.length; n++) { // Iterate through all passed windows in (i)frames
if (iframes[n].frameElement.id === id) { // Check the id of the (i)frame
result = iframes[n]; // If found the wanted id, store the window to result
}
if (!result && iframes[n].frames.length > 0) { // Check if result not found and current window has (i)frames
search(iframes[n].frames); // Call search again, pass the windows in current window
}
}
};
search(window.top.frames); // Start searching from the topmost window
return result; // Returns the wanted window if found, null otherwise
}
This function can find a frame or iframe with the passed id regardless where it is placed in the window structure. Also the function can be placed and called in any window. I'd put this to the main page (as global). If the method is needed in subwindows, just call with top.searchFrame(...).
Instead of ids, also names can be used, as long as they are also unique. In that case the id check in searchFrame() needs to be edited to name check.
In your case, first you need to give an id to the target iframe, then you can use the code for example like this:
var txtClinic = searchFrame('IFRAME_ID').document.getElementById('clinicFlag');
The method above might be a bit overkilling to get a single reference, but it's very helpful, if you have to get these cross-window references multiple times within different windows.
The specific task of yours could be done like this:
var txtClinic = parent.frames[1].frames[0].document.getElementById('clinicFlag');
names of the (i)frame are also handy to use with frames collection. Instead indices you can use names. Just always chain the reference starting from the main page, i.e. from top. For example:
var iframeWin = top.frames['frame2'].frames['iframe1'];
Useful reading:
window.top
window.frameElement
window.frames